Implements a structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position. Input parameters to StralSV (window_size, distance_cutoff, or span_size) can be varied in order to adjust the stringency with which structure fragments are selected or with which local alignments are made, thereby providing the user with flexibility in detecting similar structure fragments. Furthermore, StralSV safeguards against degradation of sequence variability data quality by enforcing structure context upon local alignments in a two-step process of identifying "qualified" hits.

Type:

Web

StralSV specifications

Unique identifier:

OMICS_16586

Interface:

Web user interface

Input data:

The coordinates of the reference structure, a list of PDB chains or a set of protein structures, the parameters for STRALSV calculations.

Funding source(s)

This work was supported by an LLNL internally funded grant through the Laboratory Directed Research and Development program, by a UC-LLNS fees grant, and partially by the National Science Foundation, through the Independent Research and Development program.